|
| Status |
Public on Jul 26, 2021 |
| Title |
LPS-treated NLRP3 reconstituted THP-1 macrophages rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: NLRP3 reconstituted
treatment: LPS
cell type: THP-1 macrophages
cell fraction: Whole cell
replicate: 3
batch: 2
|
| Treatment protocol |
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen).
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.
|
| Growth protocol |
THP-1 monocytes were maintained in RPMI 10% FCS 1% PenStrep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared with 50 ng of total cellular RNA or 30 ng of total vesicular RNA using the QuantSeq 3’ mRNA Library Prep Kit FWD for Illumina according to the manufacturer’s instructions. Libraries were sequenced on the Illumina Hiseq2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CB31_3_565_LPS
|
| Data processing |
De-multiplexing was done with bcl2fastq software v1.8.4. Sequnce software RTA v1.18.66.3 was used.
Raw reads were trimmed and Illumina adaptor sequences removed using Trimmomatic v0.36 (Bolger et al., 2014).
Trimmed reads were aligned to the Ensembl human reference genome GRCh38, with the Ensembl GRCh38 v94 GTF file, and gene-level counts were generated using STAR v2.5.3a_modified (Dobin et al., 2012).
Counts were subseuqently processed using the edgeR package v3.24.0.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-delimited table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 23, 2021 |
| Last update date |
Jul 26, 2021 |
| Contact name |
Jamie Gearing |
| Organization name |
Hudson Institute of Medical Research
|
| Street address |
27-31 Wright St
|
| City |
Melbourne |
| ZIP/Postal code |
3168 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE180707 |
Transcriptomics of THP-1 macrophages after treatment with NLRP3-induced EVs |
| GSE180709 |
Inflammasome-induced extracellular vesicles harbor distinct RNA signatures and alter bystander macrophage responses |
|
| Relations |
| BioSample |
SAMN20360376 |
| SRA |
SRX11531542 |
